The trio all missed training ahead of trip to France, and have not been included in the 19-man squad for the clash.
An adductor injury keeps Jesus out of the game, while Silva remains absent due to a knock picked up on international duty.
Gundogan played 69 minutes of the 4-0 win over West Ham United but is omitted.
"I prefer to be able to choose from all the squad but it is what it is. We have to adapt with the guys who are here," Pep Guardiola explained in Monday's press conference.
"We’re going to try to do a good game and hope the others recover as quick as possible.
"Bernardo is in the last step. I think he’ll be fit against Bournemouth. Gabriel had some muscular problem in the last action of the training session either.
"It’s not too big either but he’s not ready for tomorrow. Gundogan had a problem with the bone in his foot. We want to avoid more problems, hopefully against Bournemouth he’ll be ready."
— Manchester City (@ManCity) November 26, 2018
Youngsters Brahim Diaz and Phil Foden are in contention to feature, while Danilo returns to the fold having only played three times this season.
Brazil international Jesus has started three of City's four European games this term but will miss the chance to stake a claim for a regular Premier League place, a competition he has started in just twice.
If City can avenge the 2-1 defeat to Lyon at the Etihad Stadium in September they will secure passage for the round-of-16 as winners of Group F.
A draw will also be good enough for Pep Guardiola's men to progress if Hoffenheim and Shakhtar Donetsk also play-out a stalemate in the other group match.
Maxwel Cornet and Nabil Fekir's goals saw Lyon become the only side to beat City this season in the first meeting between the sides in Manchester.